The tree makes it clear: all non-Africans form their own independent branch from Africans. In the PCA you see that along the biggest component of variation in the genetic data the non-African groups are about the same distance from Africans. And in the ADMIXTURE analysis when you assume four ancestral populations, the Africans and non-Africans separate out cleanly excluding groups which a high likelihood of European or Arab admixture.

Neither PCA nor ADMIXTURE tells us anything about who is more distant from Africans. First of all, the clusters identified by ADMIXTURE are not phylogenetic units, nor is the pattern of splits at successive K evidence for the human phylogeny. For example, at K=2, East Eurasians split from Europeans/Africans, even though it is clear that East Eurasians do not represent a sister clade to a clade comprising of Europeans/Africans. In short ADMIXTURE (a well as frappe, STRUCTURE and assorted Bayesian clustering methods) tell us nothing about who is more distant from whom.Nor does PCA tell us anything more. Sure at the first 2 dimensions, Africans split off from non-Africans but that is insufficient to conclude that Africans are equidistant to all Eurasians. This is due to the fact that distance at the first two dimensions of PCA lower bounds total distance (a consequence of the Pythagorean theorem, no less). What does this mean? Populations that are equidistant on the (PC1, PC2) plane may be actually non-equidistant overall.

Finally, the tree argument provides evidence for Out of Africa, but it does not provide evidence for equidistance, as it not only encodes phylogenetic relationships (who is closer to whom in evolutionary terms) but also distance. It is perfectly possible that two taxa A and B may form a clade relative to a third taxon C, but that does not guarantee that A will be closer to B than to C.

As Razib notes in his newer post, it is actually Amerindians who are most distant from Africans. Here is part of a table of Fst values that I was planning to use to make that point (he uses a different one, but all studies pretty much tell the same story). It's from the recent Korean study:

Note that Yoruba (YRI) are most distant from Amerindians (AI), while all other populations fall within a very narrow range of 0.101197 to 0.119501 or about ~18% variation in distance to Yoruba.

Things become more interesting if we exclude Caucasoids (CEU) and limit ourselves to East Eurasians. Now, the range of distance from Yoruba becomes 0.108875-0.119501, or only ~10% variation in distance to Yoruba.

Yoruba are closer to (in order): to Caucasoids, East Asians, Amerindians, in that order. Distant from all, but not equidistant.

Razib advances an explanation for the Amerindian-African distance:

So what does this mean? And why is this so? I think I won’t revise my model of the out of Africa migration. I don’t think there was serious secondary migration out of Africa after the initial one (at least until recently). And yet somehow the indigenous populations of the New World are more genetically distinct. This is because of genetic drift. Specifically, a set of serial founder events, where the genetic variation was reduced and ancestral allele frequencies changed rapidly. When a population goes through a bottleneck, and then becomes isolated, it “goes its own way,” as there isn’t gene flow to requilibrate the frequencies. The push east, to Australasia and to the New World, was accompanied by founder events due to fissioning off of small groups from the main ancestral population. From what we can tell there was relatively little gene flow after the initial settlement of the New World and Oceania (actually, there may have been several waves into the New World to be fair, but it looks like there wasn’t enough Eurasian gene flow to dampen the reduction in heterozygosity caused by bottlenecks).

"Drift" gets invoked so often, so it is worthy to consider if it is responsible for the greater distance of Amerindians to Africans. "Drift" can indeed shift allele frequencies in a small population, and increase Fst. However, there are dozens of small and isolated populations throughout Eurasia, yet none of them are more distant from Africans than Amerindians are. If "drift" is responsible, then we would expect some isolated Eurasians to repeat the pattern of greater distance that Amerindians present. Good luck finding any study where any Eurasian population is more distant to Africans than (unadmixed) Amerindians are.

There is no need to invoke "drift" to explain Amerindian-African distance, as there is a simpler explanation: Amerindians, unlike Eurasians, are more distant from Africans, not because of "drift" shifting their allele frequencies, but because they lacked the opportunity for substantial gene flow with Africans.

It is worthy to revisit the Fst table: Amerindians are 1/5 further from Africans than East Asians are because they spent about 1/5 of the time since "Out of Africa" isolated from Africans. East Asians had about 60 thousand years worth of opportunities for gene flow with Africans (however limited), while the corresponding time for Amerindians is about 45-50 thousand years.

There is actual evidence for post-Out of Africa gene flow between Africa and Eurasia, but not between Africa and the Americas. It comes from the YAP marker of the human Y-chromosome. This defines the DE-YAP clade of the Y-chromosome phylogeny. This clade is absent in the Americas, but it is present in Africa, West and East Eurasia. Africa and West Eurasia share the E subclade, and East Eurasia possesses the D subclade.

What YAP tells us is that Out-of-Africa was not a one-time event: there has been subsequent gene flow linking Africa and Eurasia, and YAP is the smoking gun for this gene flow (*) There is no way around it: post-OOA men bearing YAP Y-chromosomes spread across a range spanning drom Nigeria and South Africa to the isles of Japan, but not into the Americas. These were not necessarily the only conduits for post-OOA gene flow, but they prove the existence of such gene flow.

Moreover, the greater proximity of Caucasoids to Africans can also be explained by the joint possession (by Africans and Caucasoids) of the E subclade of YAP (at the exclusion of East Asians and Negritos, who possess the D subclade).

In conclusion: the population that is most distant from Africans are Amerindians. They are more distant not because of drift but because of an earlier (10-15kya) cessation of any important gene flow between them and the rest of the species: about 1/5 less gene flow => about 1/5 more distance (relative to East Asians). Finally, this cessation of gene flow does not only make sense archaeologically, but is also evidenced genetically by the prevalence of the YAP marker, which records African-Eurasian contacts (and a nested subset of African-Caucasoid contacts) at the exclusion of Amerindians.

(*) The direction of this gene flow is contested as both Eurasian and African origin of YAP have been proposed. That's not important however, as YAP links Africa and Eurasia at the exclusion of the Americas either way.

UPDATE (Dec 24): It turns out that the greatest distance within our species is between Mbuti Pygmies and Papuans.

How about the other alternative: Maybe the YAP marker (thus DE clade) did exist in one or more of the out-of-Africa migrating human populations of the original out of Africa migrations (~60 thousand years ago) and thus spread in Eurasia in those times, but was subsequently lost among the immediate ancestors of the Amerindians during their migrations to the Americas (~10-15 thousand years ago) because of a series of drifts. Non-admixed Amerindians not only lack the DE clade but also have a very limited variety of haplogroups in general, and maybe the best explanation of this situation is drift.

Sorry, but "lacked the opportunity for substantial gene flow with Africans" is just a long winded way of describing "drift".

Drift is simply what happens when a small population is separated from its source population. If you have substantial gene flow, you probably won't have drift.

You are mistaken. Drift can operate in the presence of substantial gene flow. Add 50 Africans in a 200-strong Mongolian village and you get allele frequency shifts both because of gene flow and because of subsequent drift (in the small population of 250), or the initial settlers (50 African founders).

The presence/absence of gene flow also affects allele frequencies in the absence of drift. For example, right now gene flow is Africanizing France relative to Poland.

In no way is "lack of substantial gene flow" just a way to describe drift.

I agree with what you're saying, but it should be noted that those FST genetic distances were obtained using the pre-Cockerham & Weir FST formula. Almost all modern genetic studies use the C&W FST formula, which was shown to fit much better with simulated populations than the original version. Still, some studies occasionally use the older formula, such as the Korean study cited.

Average Joe is somewhat average in intelligence. Southern Europeans are geographically closer to Africa, and the Middle East is connected to Africa, it should not surprise that humans living in both Southern Europe and the Middle East would be more similar to Africans. By the way Northern Europeans are just a subset of Caucasoids that budded off Southern Europeans, they have as many Africans hiding in their closets as the rest of the Europeans. Southern Europe, the true Europe, has been inhabited continuously for 50,000 years. You can't say that about Northern Europe, and some parts of Northern Europe were only inhabited by I.E speaking Caucasoids from the boundary zone of Europe and Asia during the Bronze Age. In other words Joe, Northern Europeans are just blow ins, Bronze Age immigrants.

So what Dienekes is saying is that ancient Amerindians did not interbred with Ancient Africans due to being separated by ice, seawater and a large distance requiring sophisticated naval skills to traverse from either Eurasia or Africa. Disregarding the presence of haplogroups D and E in parts of Eurasia, it seems fairly reasonable to assume post OOA movements of people from Eurasia to Africa, and Africans to Eurasia.

What about the Kennewick Man and other skeletal evidence that perhaps proto-Europeans might have crossed to North American westward during the glaciations just as the Amerindian tribes verged eastward across a landbridge in the Bering Straits?

"New York Times reporter Timothy Egan calling the skeleton "Caucasian" and saying, "It adds credence to theories that some early inhabitants of North America came from European stock." But according to anthropologist Donald K. Grayson of the University of Washington, "the use of the term caucasoid really is a red flag, suggesting that whites were here earlier and Indians were here later, and there's absolutely no reason to think that."

And why not, Prof Grayson? Is this more global warming consensus-type "science?"

"I have commented before on all these admixtures, so let's summarize: Mongolia represents the eastern limit of the Caucasoid expansion, where a small Caucasoid component exists in a predominantly Mongoloid population; Southeast Asians represent a fusion of Mongoloids with "Australoid"-like indigenous populations of the tropical belt from South Asia to Micronesia; Amerindians are partially admixed with Europeans, and partially admixed with NE Asians; the latter component is marked, perhaps, by Y-chromosome haplogroup C3, and may correspondto the second wave of expansion into the Americas."

Dieneke, I'm assuming you calculated the above Fst numbers, as I can't seem to find these directly in the Korean paper.

Looking at the gap between the YRI AI number (0.143) and the next closest number YRI GJ South West Koreans (0.1195) makes me wonder if you couldn't close the gap a little by sampling the Inuit or northern groups of the Na Dene such as the Tlingit. It does appear that there are now some fairly exact dates for the Na Dene Beringia migration:

I realize that as usual there is a sampling problem. I'd also note that the samples in the Korean paper are very small (16 samples). The sample that they use to represent "Amerindians" is vague.

In any case, amongst the samples you put up, the GJ Koreans are the next most "distant" from Africa, after Amerindians.

I'm not so much interested in knowing the most distant population from Africa, as being able to date the Beringia migrations. What are the Fst numbers for Na Dene Tlingit? For Eskimo-Aleut? For the Algonquin?

So, were the Fst numbers available for the above groups, assuming Edward Vadja's hypothesis is correct, you could further support your observation that the most genetically distant group are Amerindians simply because of their isolation from admixed non-Amerindian groups. You could more precisely correlate each of the Beringia migrations with Fst number.

Exactly. And is usually invoked where the evidence doesn't fit the particular theory on offer. But once you conspire to allow 'drift' in to explain the contradiction it becomes possible to use it as a magic word, like abracadabra, to support almost any theory of human expansion and evolution you wish to champion.

"From what we can tell there was relatively little gene flow after the initial settlement of the New World and Oceania (actually, there may have been several waves into the New World to be fair, but it looks like there wasn’t enough Eurasian gene flow to dampen the reduction in heterozygosity caused by bottlenecks)."

Mine:

There may be a way to test Dienekes' hypothesis that Amerindian populations are the most genetically distant from Yorubans based on the time they have been isolated from Eurasians and Africans.

Edward Vadja, working primarily from linguistic data, suggests that there are three separate migrations into the Americas: Amerindian, Na Dene and Eskimo-Aleut, with Ameridians being the first migrators and Eskimo-Aleut being the last. The Fst distance between these groups and the Yoruba should be highest for Amerindians and lower for the Eskimo-Aleut.

There probably is not a time continuum of genetic crossover between Eurasians and Africans, but it would be interesting to see how these Fst numbers correlate with hypothesized dates for Eurasian-African genetic crossovers, if they are known.

One note of caution: Dienekes' Fst numbers for Amerindians are taken from a paper on Koreans, with the Amerindians used only as a reference point. The Amerindian sample is comprised only of 16 people.

In addition to looking at Beringia migrations, it would also be interesting to look at the "still in Siberia" suspected groups of origin for the Eskimo-Aleut and Na Dene.

"I was planning to rebut this conclusion, but Razib beat me to the punch by correcting himself that Amerindians are more distant from Africans."

And I beat both Razib and Dienekes to the punch by pointing out the greatest Fst difference between Africans and Amerindians in my comments on Razib's August 18 and July 31 posts (http://blogs.discovermagazine.com/gnxp/2010/07/daily-data-dump-friday-8/#more-5280).

I doubt, though, that either drift or gene flow can explain this. Australian aboriginals have also been separated from the rest for quite some time and they don't show higher Fst values over Amerindians. As Dienekes pointed out, there're plenty of small groups in the Old World that are subjected to drift, but they don't show similar Fst values to Amerindians. The very idea of a bottleneck in the course of the peopling of the Americas doesn't get support from several studies. See, Chakraborty and Weiss, "Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium"; Amos and Hoffman, "Evidence that two main bottleneck events shaped modern human genetic diversity").

It's more likely that there was gene flow from America to East Asia at the end of the Pleistocene/early Holocene, so American Indians are even more divergent historically than after 10,000K BP.

"The direction of this gene flow is contested as both Eurasian and African origin of YAP have been proposed. That's not important however, as YAP links Africa and Eurasia at the exclusion of the Americas either way."

Another indication, albeit indirect, that America was fully peopled at 40K, contra to the more recent timeline suggested by archaeology's Clovis First model.

...Northern Europeans are just a subset of Caucasoids that budded off Southern Europeans... Southern Europe, the true Europe, has been inhabited continuously for 50,000 years. You can't say that about Northern Europe... In other words Joe, Northern Europeans are just blow ins, Bronze Age immigrants.

Ponto,

I think I know what you are trying to say, but let's not get carried away, here. For ~20,000 years, there was a vastly larger modern human population in Northern Europe (say, north of ~46°, from France to Ukraine) than in Southern Europe. For a relatively brief ~5,000-year period around glacial maximum, those people migrated south and lived in various refuges both separated from and co-mingled with native southern Europeans. Immediately thereafter, the north was populated again, and both the north and south have been in continuous exchange ever since, yet maintaining relatively strong genetic N/S gradients.

But yes, they are all very closely related based on autosomal DNA.

Southern Europe in addition has more African inflow since the bronze age both directly, and indirectly via the middle East.

Genetic relatedness of populations has to do with how much they interbreed, so what Dienekes says makes sense in a simple straightforward way.

Concerning the disagreement between Dienekes and Vincent I should probably think more before writing but I think they both have a point:

1. Vincent is right that drift can only happen in a population with some isolation, which means the same as lack of interbreeding, during some specific period of isolation.

(It does not matter if some of the "direction" of local interbreeding comes from out of town founders who arrived BEFORE the period of relative isolation. The key period when drift happens is the period when there is relative isolation.)

2. Dienekes is of course right that drift can happen which takes a population in a "direction" which is set by founders from outside rather than inside. Why not?

But on the other hand, those founders became insiders before the draft started, and both the source population and the receiving population will continue to change after this migration, and that change will bring them further apart during the period of isolation.

No matter where the founders come from drift can not logically make two populations more genetically closely related AFTER the period of isolation than they were BEFORE.

The key moment of convergence when there are immigrations is precisely during that period of migration and inter-breeding (like in the period we have now, and in the modern populations Dienekes mentions who might be converging) not during the later period of isolation.

"Vincent is right that drift can only happen in a population with some isolation, which means the same as lack of interbreeding, during some specific period of isolation."

"Some specific period of isolation" is key here. If gene flow occurred prior to drift (a population received incoming migrants and then moved out of the "frontier" area to become isolated), then drift may erase either the effects of admixture or the effects of common descent with the parent population.

Migration 1. Haplogroup D4h3 spread into the Americas along the Pacific coast. [ Present day carries: The Chumash (California), Cayapa (Ecuador), and Yaghan(Tierra del Fuego). "On Your Knees Cave Man", who died in Southeastern Alaska 10 kya, carried D4H3. The Chumash were, until about 100 ya, an expert an expert whaler and canoe building culture. There is some evidence that the coastal Chumash are related to other distinctive Pacific coast canoe cultures through a specific mtDNA haplogroup A mutation, to the Nuu Chah Nuulth, Haida, and Bella Coola peoples of coast British Columbia. See "Mitochondrial DNA and Prehistoric Settlements: Native Migrations on the Western Edge of North America", Jason A. Eshleman, et. al.]

Migration 2. X2a entered through the ice-free corridor between the Laurentide and Cordilleran icesheets. [ Highest incidence of X2a occurs in Algonquian speakers, a cohesive indigenous group with a distinctive appearance, culture and language. ]

Time estimates for both of these migrations are approximately 15-17 kya.

Migration 3. "The presence of group B deletion haplotypes in East Asian and Native American populations but their absence in Siberians raises the possibility that haplogroup B could represent a migratory event distinct from the one(s) which brought group A, C, and D mtDNAs to the Americas."

Time estimate: 17-34 kya

"Distribution: Group B mtDNAs are dispersed throughout the Amerinds of North, Central and South America at continental frequencies of 19%, 33% and 18%, respectively."

Proposes an early expansion along coastal Siberia and Americas.

**********************************

An important paper that disputes the idea of more than one Paleo-Indian migration:

"More recently, haplogroups A, B, C, D, andX, assigned both by restriction analysis and CR sequencing, haveall been reported in an Altai population from southern Siberia(Derenko et al. 2001), where archaeological sites dating to atleast 20,000 yr B.P. are found (Goebel 1999). The ancestors ofthis population represent the only known surviving possiblesource for peopling of the New World via a single migration."

Single A, B, C, D and X migration as proposed by David Glenn Smith, et. al.

Some thoughts:

Based on the facial distinctiveness of Algonquin, Plains Indian, Central American and Pacific Coast groups, as well as cultural signatures, I believe it is improbably that the Americans were peopled by a single group.

However, although I do not concur with David Glenn Smith, et. al. regarding a single migration, I appreciate the careful examination of method and data given in this paper.

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